Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Blood

Cell type

Hematopoietic Stem Cells

MeSH Description

Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Sample

source_name

hematopietic progenitor and stem cells

antibody

H3K4me3

treatment

DMSO

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

cells were fixed with 1% formaldehyde and sonicated with Covaris E220. Sonicated chromatin were then incubated with antibody against H3K27me3(Cell Signaling, #9733), H3K4me3(Cell Signaling, #9571) overnight. Protein A/G beads (ThermoFisher) were added to the sonicated chromatin for 2 hours. After washes with low-salt, high-salt and LiCl wash buffer. Following washes, beads were tagmented by Illumina tagmentation enzyme mix for 10 mins at 37 °C. After the tagmentation reaction stopped and the wash of beads, pull-downed DNA was de-crosslinked with Proteinase K (Zymo Research) at 55 °C for 3 hours. Pull-downed DNA was extracted by DNA clean and concentration kit (Zymo Research). PCR amplification was directly performed, and libraries were cleaned by home made SeraMag beads and sequenced with Illumia NextSeq Platform.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

40893332

Reads aligned (%)

95.9

Duplicates removed (%)

55.4

Number of peaks

9163 (qval < 1E-05)

hg19

Number of total reads

40893332

Reads aligned (%)

94.8

Duplicates removed (%)

56.6

Number of peaks

9284 (qval < 1E-05)